The Molecules of Life

• All living things are made up of carbohydrates, proteins, lipids, nucleic acids

• Macromolecules: Complex and large molecules

  • Function/properties derive from the order and number of atoms

• Polymer: Long molecule consisting of repeating building blocks that form long chains

  • Including proteins, nucleic acid, and carbohydrates

  • Fats do not have repeating building blocks

• Monomer: The units/building blocks make up polymers.

==The Synthesis and Breakdown of Polymers ==

• Enzymes: specialized macromolecules that aid in “speeding up” reactions such as those that make or break down polymers.

  • Doesn’t literally speed up the process, it just decreases the amount of energy required to initiate the reaction.

• Dehydration synthesis: This occurs when two monomers bond together through the loss of a water molecule.

• Hydrolysis: Using pressure to break the bond and adding a water molecule to the free bonds.

  • Disassembles polymers

  • Without water, those empty bonds can virtually bond with anything else and potentially become poison.

==The Diversity of Polymers ==

• Variety is created by slightly modifying polymers (from a small set of monomers)

  • Ex. Glycogen is broken down into the cell for energy and the starch is stored as fat

• Least to greatest variety = within the same species vs. between species

Carbohydrates & Sugars

• Carbohydrates include sugars and can vary from monosaccharides (simple sugars) to polysaccharides (macromolecules, composed of many sugar building blocks)

• Almost everything in the body can be broken down to make carbohydrates

• Most common sugar = glucose (C6H12O6)

• Distinct in the position of the carbonyl (as aldose or ketose) and the number of carbons

  • In multiples of CH2O

• Visually, alpha and beta glucose only physically differentiate based on how they react in water

• Aldoses: Aldehyde sugars

• Ketoses: Ketone sugars

• Trioses: 3 carbon sugers (C3H6O3)

• Pentoses: 5 carbon sugars (C5H10O5)

• Hexoses: 6 carbon suagrs (C6H12O6)

• In alpha glucose: 3rd carbon is the switch, but the 4th carbon is what changes between glucose and galactose (flipped), on first carbon - hydrogen is up, (aldose on 1).

• In beta glucose: 3rd carbon switch, but 1st carbon is what changes between alpha and beta glucose

• In fructose: 5 carbons (#1 is the Ch2OH) with OH bonded to it, switch on 4, ends with CH2OH bonded with H (Ketose on 2nd)

• Maltose: alpha glucose + alpha glucose

• Sucrose: alpha glucose + fructose

• Lactose: alpha glucose + galactose

• In aqueous solutions, many sugars form rings

• Monosaccharides serve as a major fuel for cells and as raw material for building molecules

• Disaccharide (oligosaccharide): Occurs when two monosaccharides bond together from dehydration synthesis (this bond = glycosidic linkage = not an ether bond)

  • Not a polymer

• Glycosidic bonds: covalent bonds that bond monosaccharides together to form a disaccharide, oligosaccharide, or polysaccharide.

  • Alpha: Below the plane (parallel)

  • Beta: Above the plane (zigzag)

• Trisaccharide: a polymer and a polysaccharide

  • Alpha bonds: :] (direct bonding)

  • Beta bonds: :> (zig zag bonding, alternating pattern between molecules)

Polysaccharides

• Polysaccharides: Contain a large number of monosaccharide units bonded to each other by a series of glycosidic bonds

  • The polymers of sugar have storage and structural roles

• Artificial sugar is bigger = increased chances of clots

• Constant sugar consumption = sugar molecules scratches against capillaries (forms scabs in blood vessels)

• Structure and function are dictated by the number of atoms (monomers) and placements of its glycosidic linkages

• Storage:

  • Starch (Storage polysaccharide for plants): Has storage for glucose monomers (plant version of glycogen)

    • Surplus starch stored in chloroplasts and other plastids

    • The simplest form is amylose

  • Glycogen (Storage polysaccharide for animals): Has storage for glycogen in liver and muscle cells

    • Hydrolysis of glycogen in these cells releases glucose when there is a sugar demand

    • Has much more branches than starch because it must be easily compressed into cells

  • Cellulose has beta bonds

• Structure:

  • The polysaccharide cellulose = a major component of the tough wall of plant cells

  • Like starch, cellulose is a polymer of glucose, but the glycosidic linkages differ

  • The difference is based on two ring forms for glucose: alpha (α) and beta (β)

    • Ex. hard shell of a bug

  • Chitin: found in the exoskeleton of arthropods

    • Also provides structural support for the cell walls of fungi (why it’s chewy)

• Differences:

  • Structural polysaccharides are made up of beta glucose monomers (beta glycosidic linkages), whereas storage polysaccharides have alpha glucose monomers (alpha glycosidic linkages)

  • Starch (alpha config.) is helical (spiral)

  • Cellulose (beta config.) is straight and unbranched

    • Certain hydroxyl groups on cellulose monomers can hydrogen-bond with hydrogen on parallel cellulose monomers

  • Enzymes that digest starch by hydrolyzing alpha linkages cannot hydrolyze beta linkages of cellulose

  • Cellulose in human food passes by the digestive tract as “insoluble fiber”

  • Some microbes digest cellulose and form symbiotic relationships with other animals (ex. cows)

• *Individual glucose molecules are macromolecules, but not polysaccharides

Lipids

• Lipids are the one class of large biological molecules that do not include true polymers

  • Not considered polymers (polymers are different from polysaccharides, which are specific to sugar)

• The unifying feature of lipids is that they mix poorly, if at all, with water

• Lipids consist mostly of hydrocarbon regions

• The most biologically important lipids are fats, phospholipids, and steroids

• Good fats have at least 1 double bond (liquid in room temp)

Fats

• Constructed from fatty acids and glycerol

  • Glycerol: 3-carbon alcohol with a hydroxyl group attached to every carbon

  • Fatty acid: Carboxyl group attached to a long carbon skeleton

• Forming as ester linkage = esterfication (-COO)

• Separates from water because water molecules hydrogen-bond to each other, which excludes the fats

  • Fats separate from water immediately

• In a fat, 3 fatty acids are joined to a glycerol by an ester linkage, creating a triacyglycerol, or triglyceride

• The fatty acids in a fat can be all the same or of 2 or 3 diff kinds

• Fatty acids vary in length (number of carbons) and the number and locations of double bonds

• Unsaturated fatty acids have more than one double bond (1+)

  • In unsaturated fat = the flat part (cis-double bond) is not all bonded to hydrogens (can be bonded to anything)

  • Fats made from unsaturated fatty acids are called unsaturated fats or oils and are liquid at room temperature

  • In the structural formula, the zigzag is saturated, and the zigzag with a flat part is unsaturated.

  • More than 1 double-bond = polyunsaturated lipids (v healthy)

  • Plant fats and fish fats are usually unsaturated

• Saturated fats

  • Made from fats with saturated fatty acids and are solid at room temperature

  • Most animal fats are saturated

  • Healthy in small quantities

    • A diet rich in saturated fats may contribute to cardiovascular disease through plaque deposits Including genetics, bodily systems, habits, etc. Not just saturated fats.

  • Hydrogenation: The process of converting unsaturated fats to saturated fats by adding hydrogen

    • Hydrogenating vegetable oils also creates unsaturated fats with trans-double bonds

    • These trans-fats may contribute more than saturated fats to cardiovascular disease

• Hydrogen or OH on carbon will switch sides under pressure/heat and become a trans fat (body does not like this structure)

• To become a trans fat, the fat must be unsaturated for the double bond

• Major function of fats is energy storage

• Humans and other animals store their long-term food reserves in adipose cells

• Adipose tissue (fat tissue) also cushions vital organs and insulates the body

==Phospholipids ==

• Two fatty acids and a phospholipid are attached to a glycerol

  • Fatty acids are hydrophobic, but phospholipid and its attachments form a hydrophilic head

  • Choline, phosphate, glycerol

• Charged head bonds with other things

• Bent leg is unsaturated, straight is saturated so that they stay together but still allow different molecules to go ther (both straight = too tight, both bent = too loose and has no protected layer)

• If both legs were straight, it would take A LOT of energy to break apart or multiply

• Phospholipids added to water self-assemble into double-layered sheets called a bilayer

• Surface of a cell:

  • Phospholipids are arranged in a bilayer, with the hydorphobic tails pointed towards the interior

  • Phospholipid bilayer forms a boundary between the cell and its external environment

Steroids

• Lipids characterized by a carbon skeleton consisting of four fused rings

• Cholesterol: prevalent in animal cell membranes and a precursor to which other steroids are synthesized

• High level may cause cardiovascular disease

• Steroid backbone (4 fused rings, one with a double-bond and one as a pentagon)

Protein

• Account for 50%+ dry mass of most cells

  • Responsible for cellular communication, immune system (antibodies specific towards each antigen), and movement, storage, structural support, transportation

• All proteins (when not needed) will be broken down into urea

  • They appear to “speed up” chemical reactions because they reduce the amount of input energy required to kick start the reaction

• Always 1 less water molecule than sugar molecules bonded together (in starch)

• Types of Proteins:

  • Enzymatic Proteins

    • Selective acceleration of chemical reactions

    • Ex. Catalyzing the breakdown of food molecules

  • Defensive Proteins

    • Protection against disease

    • Ex. Antibodies help destroy viruses and bacteria

  • Storage Proteins

    • Storage of amino acids

    • Ex. Casein, protein of milk.

  • Transport Proteins

    • Transport substances

    • May need energy for transport

    • Ex. Hemoglobin

  • Hormonal Proteins

    • Coordination of an organism’s activities

    • Ex. Insulin regulates blood sugar concentrations (by opening channels for sugar to enter cells)

  • Receptor Proteins

    • Response of cell to chemical stimuli

    • Ex. Receptors in nerve cells detect signals from other nerve cells

  • Contractile and motor Proteins

    • Movement

    • Ex. Actin and myosin are responsible for the contracting and relaxing of muscles

  • Structural Proteins

    • Support & keep us moving (connective tissue)

    • Keratin in hair or silk fibers in spider webs

• Enzymes act as biological catalysts that reduce the activation energy for chemical reactions

  • Can be used over and over again

• Proteins are all constructed from the same amino acids

• Polypeptide: Unbranched polymer of amino acid built from those amino acids (DNA will tell protein to make them a certain way)

• Protein: A biologically functioning molecule that contains one or more of those polypeptides

==Amino Acid Monomers ==

• Organic molecules with animo group and carboxyl group

• Differ because of differing R groups:

  • Polar side chains (hydrophilic)

  • Electrically charged side chains (hydrophilic)

    • Acid

    • Base

  • Non-polar side chains (hydrophobic)

• Amino acids have peptide bonds

  • Different monomers are bonded with dehydration synthesis

• Polypeptide: polymer of amino acids

  • Can range from a few - 1000+ monomers

  • Have a carboxyl end/c-terminus (COOH) and an amino end/n-terminus (NH2)

Protein Structure and Function

• The activity comes from its specific architecture (sequence of amino acid)

  • Polypeptides are specifically coiled, twisted, folded etc.

• The peptide bond must form immediately or else the amino acid will be broken apart or recycled

• The function of a protein usually depends on its ability to recognize and bond to other some other molecule

4 Levels of Protein Structure:

• Primary

  • The unique sequence of amino acids

  • Determined by inherited genetic information

  • DNA → RNA → Polypeptides (give us our unique characteristics)

• Secondary

  • Found in most proteins - folds and coils in the polypeptide chain

    • Caused by hydrogen bonds between the repeating components of the polypeptide backbone

  • Can have alpha helix and beta pleated sheets held loosely together

• Tertiary

  • Interactions among various side chains (R groups) cause the shape instead of the backbone interactions

    • R group interactions: hydrogen bonds, ionic bonds, hydrophobic interactions, LDF

    • Strong covalent bonds (disulfide bridges) may reinforce the protein’s structure

  • Proteins must be at least at this stage

  • More compressed together

• Quaternary

  • Consists of multiple polypeptide chains (2+ form one macromolecule)

    • Ex. Collagen (3 polypeptide ropes), Hemoglobin (2 alpha and 2 beta subunits)

  • Combinations of tertiary structures

• Like high school grades (+ interactions, qualities per grade)

• Structure Changes are caused by:

  • Changed primary structure

  • TEMPERATURE

  • PH

  • Salt concentrations

  • Differing physical or chemical conditions

• Changed protein shape and function = denaturation (biologically inactive)

• Proteins can revert to their original form and purpose when placed back into ideal environments

Diseases and Protein Folding

• Sickle Cell Disease: A Change in primary Structure

  • A slight change in the protein’s primary structure can change its form and function

  • Sickle cell disease comes from a changed amino acid in Hemoglobin

    • Red blood cells aggregate (combine) into chains and deform into a sickle-shape

    • Normally, the proteins remain independent, but in this disease, they stick together to form a chain which reduces the transportation of oxygen

    • On the 6th amino acid Glu → Val

• Hard to predict a protein’s structure from the primary structure (usually go through various stages before becoming stable)

  • Alzheimer’s, Parkinson’s, etc.

Nucleic Acids

• Store, transmit, express hereditary information

• Has carboxyls, amino acid sequence in polypeptide is programmed by the gene

• Genes consist of DNA (a nucleic acid w/ nucleotide monomers)

• 2 types of nucleic acids

  • DNA

    • Directs its own creation

    • Directs the creation of mRNA, and therefore controls protein synthesis

  • RNA

    • Dominant part of DNA is copied to make RNA

• Ribosomes make and are proteins

• This is gene expression

  • Recessive is coiled tightly so that its data is not replicated

  • Dominant genes unwind so that they can be easily replicated and expressed

• Stages of Synthesis:

  • Synthesis of mRNA

    • mRNA made out of freed bases in the nucleus (DNA code determines code of RNA)

    • mRNA exits nucleus

  • Movement of mRNA in cytoplasm

    • Ribosome takes mRNA and reads the code

    • tRNA brings amino acids read from the “recipe” to the ribosome

  • Synthesis of Protein

    • tRNA carries amino acids to ribosomes

    • A chain of amino acids is formed

    • Protein is formed out of amino acids

• mRNA = brings info from DNA to cytoplasm

• tRNA = type or RNA that has 1 particular amino acid to it (drop off the correct amino acid to form polypeptide chains)

  • Amino acids connected to tRNA

• rRNA = specifically makes ribosomes from ribosomes

• RNA = kinda like recipes read to make stuff

Each gene along a DNA molecule directs the synthesis of mRNA

• mRNA interacts with protein-synthesizing machinery in the cell to form polypeptides

• Flow of genetic information = DNA → RNA → polypeptides (protein)

Components of Nucleic Acids

• Nucleic acids = polymers called polynucleotides

• Each polynucleotide is made of monomers called nucleotides

  • Free-floating = 3 phosphate group

  • Part of a DNA = 1 phosphate group

    • Other 2 are used to fuel the combining of nucleotides

• Nitrogenous base, pentose sugar, and phosphate group

• The portion of a nucleotide without the phosphate group (so just sugar and nitrogenous base) is called the nucleoside

• Nitrogenous bases:

  • Pyrimidines (cytosine, thymine, uracil - “y am i single?”)

    • Thymine is only in DNA because of the amino acid code

    • Uracil is only n RNA

    • Has a 6 membered rings (single)

    • Backbone = phosphodiester bond (2 ester bonds with phosphate group)

  • Purines (adenosine, guanine)

    • Has a 6 membered rings fused into a 5 membered ring (double)

  • A double bond with T, C triple bond with G

• DNA has deoxyribose sugar, RNA has ribose

Nucleotide Polymers

• Nucleotides are linked by a phosphodiester linkage to make a polynucleotide

• Phosphodiester linkage = a bond that bonds the sugars of 2 nucleotides

  • Created a sugar backbone unit with nitrogenous bases as appendages

  • Sequence for DNA or mRNA polymer is unique for each gene

• DNA:

  • Double-helix

  • One side of the strand is gene

  • Labeled 5’ and 3’ on opposite ends (phosphate and hydroxyl respectively)

  • A-T and C-G make it possible for identical copies of each DNA molecule to be made when a cell is preparing to divide

• RNA:

  • Single-stranded

  • Complementary pairing can still occur (if the RNA is folded in on itself)

  • Thymine is replaced by uracil, so A and U pair together

Genomics and proteomics have transformed biological inquiry and applications

• Biologists wanted to “decode” genes by looking at their base sequences

• Developed sequencing methods from Human Genome Project